Contacts of the helix formed by residues 67 - 83 (chain A) in PDB entry 3NIE
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 67 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A ARG 5.0 1.2 + - - -
64A MET 4.1 3.5 - - - +
66A GLU* 1.3 80.3 - - + +
68A LEU* 1.3 65.0 + - - +
69A ILE* 3.0 24.1 + - - +
70A ASP* 3.4 30.1 + - + +
71A CYS* 3.0 24.1 + - - +
214A THR* 2.7 32.9 + - - +
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Residues in contact with LEU 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A PHE* 3.0 40.8 - - + +
66A GLU 4.0 2.4 + - - +
67A ASP* 1.3 74.1 + - - +
69A ILE* 1.3 65.4 + - + +
70A ASP 3.3 0.2 - - - -
71A CYS* 3.5 8.1 - - + +
72A LYS* 3.0 28.2 + - - +
396A LEU 3.7 23.1 - - - +
397A SER* 4.5 1.1 - - - -
398A GLU* 3.7 28.0 - - + +
401A LEU* 3.9 11.8 - - + +
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Residues in contact with ILE 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A ASP* 3.0 13.2 + - - +
68A LEU* 1.3 81.9 - - + +
70A ASP* 1.3 60.5 + - - +
72A LYS* 3.4 11.9 + - + +
73A ARG* 3.1 24.3 + - - +
179A ARG* 6.3 1.3 - - - +
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Residues in contact with ASP 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A TYR* 3.9 20.9 + - + -
63A ARG 5.9 2.9 - - - +
64A MET* 4.8 2.2 - - - +
67A ASP* 3.4 32.4 + - + +
68A LEU 3.3 0.2 - - - -
69A ILE* 1.3 79.3 - - - +
71A CYS* 1.3 67.3 + - - +
73A ARG* 3.0 24.4 + - - +
74A ILE* 3.2 15.6 + - + +
214A THR* 4.2 4.2 + - - -
216A HIS* 2.8 35.1 + - - -
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Residues in contact with CYS 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A MET* 3.2 23.8 + - - +
65A PHE* 3.4 35.7 - - - -
67A ASP 3.0 12.1 + - - +
68A LEU* 3.5 16.4 - - + +
69A ILE 3.4 0.2 - - - -
70A ASP* 1.3 75.7 - - - +
72A LYS* 1.3 63.2 + - - +
74A ILE* 3.2 6.8 + - - -
75A LEU* 3.1 17.3 + - - +
401A LEU* 3.9 14.6 - - + -
405A PHE* 3.8 23.0 - - - -
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Residues in contact with LYS 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A LEU 3.0 17.8 + - - +
69A ILE* 3.7 12.8 - - + +
71A CYS* 1.3 74.1 - - - +
73A ARG* 1.3 57.7 + - - +
75A LEU* 3.2 8.9 + - - +
76A ARG* 2.9 48.4 + - - +
179A ARG* 5.4 1.1 - - - +
390A PHE* 3.4 37.2 - - + -
391A ASP 3.2 4.2 + - - -
392A ASP 2.4 31.1 + - - -
394A MET 2.8 23.1 + - - +
396A LEU* 5.2 3.6 - - + -
401A LEU* 4.4 15.6 - - + +
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Residues in contact with ARG 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A TYR* 3.4 59.7 - - - +
61A VAL* 6.2 0.2 - - - +
69A ILE 3.1 13.4 + - - +
70A ASP* 3.0 15.7 + - - +
72A LYS* 1.3 76.1 - - - +
74A ILE* 1.3 60.1 + - - +
76A ARG* 3.2 3.2 + - - +
77A GLU* 3.0 41.5 + - - -
156A ASP* 5.5 2.0 + - - -
174A ASP* 3.7 16.3 + - - -
176A GLY* 3.3 42.8 - - - +
177A LEU* 4.6 21.7 - - + +
430A ANP 3.3 32.1 + - - -
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Residues in contact with ILE 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A TYR* 5.4 5.8 - - + -
61A VAL* 3.1 40.6 - - + -
64A MET* 3.7 33.9 - - + -
70A ASP* 3.2 15.5 + - + +
71A CYS* 3.2 7.3 + - - +
73A ARG* 1.3 85.4 - - - +
75A LEU* 1.3 65.5 + - - +
77A GLU* 3.5 14.9 + - - +
78A ILE* 3.0 22.9 + - + +
107A LEU* 3.9 9.0 - - + -
109A ILE* 4.1 16.2 - - + -
405A PHE* 3.9 9.9 - - + -
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Residues in contact with LEU 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A CYS 3.1 8.4 + - - +
72A LYS* 3.5 9.4 - - - +
74A ILE* 1.3 76.7 - - - +
76A ARG* 1.3 52.8 + - - +
78A ILE* 3.3 2.1 + - + -
79A THR* 2.8 50.7 + - + +
390A PHE* 3.8 19.1 - - + -
401A LEU* 3.8 24.7 - - + +
404A ILE* 3.5 45.3 - - + +
405A PHE* 3.4 50.1 - - + +
408A GLU* 4.8 1.8 - - + -
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Residues in contact with ARG 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A LYS* 2.9 42.9 + - - +
73A ARG* 3.2 8.9 + - - +
75A LEU* 1.3 73.9 - - - +
77A GLU* 1.3 66.3 + - - +
79A THR* 3.1 5.0 + - - -
80A ILE* 3.1 41.0 + - + +
175A PHE 4.1 1.8 - - - -
176A GLY* 3.6 18.6 + - - +
178A ALA 3.0 33.7 + - - +
179A ARG* 3.0 36.6 - - - +
180A THR 5.4 0.2 - - - +
388A LEU* 4.4 11.9 - - + +
390A PHE* 3.8 23.1 + - + -
391A ASP* 5.0 0.4 - - - +
392A ASP* 3.2 27.9 + - - +
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Residues in contact with GLU 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A LYS* 2.5 43.9 + - - +
61A VAL* 5.6 0.2 - - - +
73A ARG* 3.0 27.4 + - - +
74A ILE* 3.7 16.8 - - - +
76A ARG* 1.3 75.1 - - - +
78A ILE* 1.3 64.9 + - + +
80A ILE* 4.1 1.2 - - - +
81A LEU* 3.2 39.9 + - + +
109A ILE* 4.4 12.4 - - - +
111A LEU* 5.4 2.6 - - - +
174A ASP* 4.4 11.4 + - - -
175A PHE* 3.9 15.4 - - - +
176A GLY* 3.7 20.7 - - - +
430A ANP 4.4 0.2 + - - -
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Residues in contact with ILE 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A ILE* 3.0 25.2 + - + +
75A LEU* 3.8 5.6 - - + +
77A GLU* 1.3 78.9 - - + +
79A THR* 1.3 61.7 + - + +
81A LEU* 3.5 2.1 + - + -
82A ASN* 3.1 28.2 + - - +
92A LEU* 3.5 11.5 - - + +
95A LEU* 3.6 36.6 - - + -
107A LEU* 4.6 4.7 - - + -
109A ILE* 3.3 54.5 - - + -
405A PHE* 4.8 6.7 - - + -
408A GLU* 4.3 14.8 - - + +
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Residues in contact with THR 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A LEU* 2.8 43.8 + - + +
76A ARG* 3.1 10.4 + - - -
78A ILE* 1.3 68.2 - - - +
80A ILE* 1.3 67.5 + - - +
82A ASN 3.6 0.5 + - - -
83A ARG* 2.7 43.9 + - - +
388A LEU* 3.7 7.9 - - - +
389A PRO* 3.7 30.3 - - + -
390A PHE* 3.6 9.4 - - + -
404A ILE* 4.4 0.2 - - + -
408A GLU* 3.7 23.3 - - + -
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Residues in contact with ILE 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A ARG* 3.1 22.3 + - + +
77A GLU 4.1 2.2 - - - +
79A THR* 1.3 82.0 + - - +
81A LEU* 1.3 63.2 - - - +
83A ARG* 3.0 13.3 + - - +
84A LEU* 3.2 28.4 + - + +
152A ILE* 4.5 11.4 - - + -
175A PHE* 3.7 37.2 - - + +
178A ALA* 3.5 32.8 - - + -
179A ARG 6.2 0.4 - - - -
386A ILE* 4.3 10.4 - - + +
388A LEU* 3.8 28.3 - - + -
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Residues in contact with LEU 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A GLU* 3.2 37.1 + - + +
78A ILE* 4.1 3.4 - - - +
80A ILE* 1.3 78.9 - - - +
82A ASN* 1.3 61.4 + - - +
83A ARG 3.4 0.7 + - - -
84A LEU* 3.5 20.4 + - + +
89A ILE* 3.7 20.4 - - + -
90A ILE* 3.5 34.2 - - + +
91A ARG* 5.5 0.2 - - - -
92A LEU* 4.0 24.2 + - + +
109A ILE* 5.6 1.3 - - + -
111A LEU* 3.9 27.8 - - + -
173A CYS* 4.8 0.7 - - + -
174A ASP 5.0 5.4 - - - +
175A PHE* 3.8 19.5 - - + -
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Residues in contact with ASN 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A ILE 3.1 19.6 + - - +
79A THR 3.7 5.8 - - - +
81A LEU* 1.3 76.8 - - - +
83A ARG* 1.3 64.0 + - - +
84A LEU 3.5 2.8 + - - +
85A LYS* 5.6 2.6 - - - +
92A LEU* 3.4 15.8 - - + +
408A GLU* 3.0 27.9 + - - +
411A SER* 3.2 25.1 + - - -
412A PHE* 3.4 23.5 - - - -
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Residues in contact with ARG 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A THR* 2.7 37.3 + - - +
80A ILE 3.0 5.8 + - - +
82A ASN* 1.3 83.6 - - + +
84A LEU* 1.3 60.9 + - - +
85A LYS* 4.3 6.0 + - - +
386A ILE* 3.2 34.2 - - + +
387A ILE 3.3 26.5 + - - +
388A LEU* 4.2 8.7 - - - -
389A PRO* 3.5 24.7 - - - +
408A GLU* 2.7 43.6 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il